Merge pull request #1254 from nipreps/docs/freesurfer-dependency

ENH: Improve documentation and logging of *SynthStrip*'s model

docs/source/install.rst

@@ -62,23 +62,48 @@ Execution system dependencies
 If you are using a a `Neurodebian <http://neuro.debian.net/>`_ Linux distribution,
 installation should be as easy as::
 
-  sudo apt-get install fsl afni ants
+  sudo apt-get install afni ants
   sudo ln -sf /usr/lib/ants/N4BiasFieldCorrection /usr/local/bin/
 
 After installation, make sure that all the necessary binaries are added to the ``$PATH`` environment
 variable, for the user that will run ``mriqc``.
 
-Please note that MRIQC requires Freesurfer's Synthstrip tool. If you already have Freesurfer installed,
-you can get the requirements with: ::
-
-  wget https://github.com/freesurfer/freesurfer/blob/dev/mri_synthstrip/synthstrip.1.pt -P <path_to_your_freesurfer_dir>/models/
+Otherwise, you can follow each software installation guide:
+`AFNI <https://afni.nimh.nih.gov/afni/doc/howto/0>`_,
+and `ANTs <http://stnava.github.io/ANTs/>`_.
 
 .. warning::
 
-        You will get the error `The 'model' trait of a _SynthStripInputSpec instance must be a pathlike object or string representing an existing file, but a value of '<undefined>' <class 'str'> was specified.`
-        if you do not install the previous Freesurfer requirement.
+    Please note that *MRIQC* 22.0.0 and later requires Freesurfer's *SynthStrip* tool.
 
-Otherwise, you can follow each software installation guide:
-`FSL <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation>`_,
-`AFNI <https://afni.nimh.nih.gov/afni/doc/howto/0>`_,
-and `ANTs <http://stnava.github.io/ANTs/>`_.
+Please also install *FreeSurfer* (above 7.2) using `their guidelines <https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall>`__.
+If your *FreeSurfer* version is older than 7.2, then you can get *MRIQC*'s requirements with::
+
+  wget https://github.com/freesurfer/freesurfer/blob/dev/mri_synthstrip/synthstrip.1.pt -P ${FREESURFER_HOME}/models/
+
+.. danger::
+
+        You will get the following error if you do not install *SynthStrip*'s requirement::
+
+          The 'model' trait of a _SynthStripInputSpec instance must be a pathlike object or string representing an existing file, but a value of '<undefined>' <class 'str'> was specified.`
+
+        If the *SynthStrip* requirement was downloaded, please make sure your environment has defined the variable ``$FREESURFER_HOME`` and that it is pointing at the right directory::
+
+          echo $FREESURFER_HOME
+
+        If the ``$FREESURFER_HOME`` environment variable is defined, check whether the model file is available at the expected path::
+
+          $ stat $FREESURFER_HOME/models/synthstrip.1.pt 
+            File: /opt/freesurfer/models/synthstrip.1.pt
+            Size: 30851709    Blocks: 60264      IO Block: 4096   regular file
+          Device: fd00h/64768d  Inode: 12583379    Links: 1
+          Access: (0644/-rw-r--r--)  Uid: (    0/    root)   Gid: (    0/    root)
+          Access: 2024-04-09 11:13:29.091893354 +0200
+          Modify: 2023-01-20 09:39:54.284056264 +0100
+          Change: 2023-01-20 09:39:54.284056264 +0100
+           Birth: 2023-01-20 09:39:54.224056213 +0100
+
+        If *SynthStrip*'s model file is not present, the output will look like::
+
+          $ stat $FREESURFER_HOME/models/synthstrip.1.pt
+          stat: cannot statx '/opt/freesurfer/models/synthstrip.1.pt': No such file or directory

mriqc/cli/run.py

@@ -142,6 +142,19 @@ def main():
                 config.nipype.nprocs,
             )
 
+        # Check synthstrip is properly installed
+        if not config.environment.synthstrip_path:
+            config.loggers.cli.warning(
+                (
+                    'Please make sure FreeSurfer is installed and the FREESURFER_HOME '
+                    'environment variable is defined and pointing at the right directory.'
+                ) if config.environment.freesurfer_home is None
+                else (
+                    f'FreeSurfer seems to be installed at {config.environment.freesurfer_home},'
+                    " however SynthStrip's model is not found at the expected path."
+                )
+            )
+
         if mriqc_wf is None:
             sys.exit(os.EX_SOFTWARE)
 

mriqc/config.py

@@ -205,6 +205,13 @@
             ).decode().strip().split(' ')[-1]
             _memory_gb = float(_mem_str) / (1024.0**3)
 
+# Check for FreeSurfer's SynthStrip model
+_fs_home = os.getenv('FREESURFER_HOME', None)
+_default_model_path = Path(_fs_home) / 'models' / 'synthstrip.1.pt' if _fs_home else None
+
+if _fs_home and not _default_model_path.exists():
+    _default_model_path = None
+
 
 class _Config:
     """An abstract class forbidding instantiation."""
@@ -281,12 +288,16 @@ class environment(_Config):
     """A string representing the execution platform."""
     free_mem = _free_mem_at_start
     """Free memory at start."""
+    freesurfer_home = _fs_home
+    """Path to the *FreeSurfer* installation (from ``FREESURFER_HOME`` environment variable)."""
     overcommit_policy = _oc_policy
     """Linux's kernel virtual memory overcommit policy."""
     overcommit_limit = _oc_limit
     """Linux's kernel virtual memory overcommit limits."""
     nipype_version = get_version('nipype')
     """Nipype's current version."""
+    synthstrip_path = _default_model_path
+    """Path to *SynthStrip*'s model weights (requires *FreeSurfer*)."""
     templateflow_version = get_version('templateflow')
     """The TemplateFlow client version installed."""
     total_memory = _memory_gb

mriqc/interfaces/synthstrip.py

@@ -21,9 +21,6 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """SynthStrip interface."""
-import os
-from pathlib import Path
-
 from nipype.interfaces.base import (
     CommandLine,
     CommandLineInputSpec,
@@ -33,11 +30,13 @@
     traits,
 )
 
-_fs_home = os.getenv('FREESURFER_HOME', None)
-_default_model_path = Path(_fs_home) / 'models' / 'synthstrip.1.pt' if _fs_home else Undefined
+from mriqc import config
 
-if _fs_home and not _default_model_path.exists():
-    _default_model_path = Undefined
+_model_path = (
+    str(config.environment.synthstrip_path)
+    if config.environment.synthstrip_path is not None
+    else Undefined
+)
 
 
 class _SynthStripInputSpec(CommandLineInputSpec):
@@ -51,7 +50,7 @@ class _SynthStripInputSpec(CommandLineInputSpec):
         False, usedefault=True, argstr='-g', desc='Use GPU', nohash=True
     )
     model = File(
-        str(_default_model_path),
+        _model_path,
         usedefault=True,
         exists=True,
         argstr='--model %s',